Setting up your house to ward off long term ninja infestations. It's considered impossible to keep ninjas out entirely. In fact, attempting to do so can attract their attention and just make the problem worse.

1) Coat the walls and ceilings with steel backed teflon. If the steel isn't thick enough, they can still use their claws. Make sure it's at least a 1/4 inch thick.
2) Install random rotating magnets. This makes it difficult to throw shurikens accurately.
3) Set up a DVD of old "Kung Fu" reruns in infinite reply. Warning: This may cause Seppuku incidents, which are really messy. Take my word on it. Spread plastic in front of the TV.

Avoid using pirates. I know it's tempting, but they're worse than ninjas (really loud and smelly and treasure chests are hard to find).

Bob: Where were you last weekend?
Bill: Sorry, spent all day Saturday Ninja Proofing.